To analyze the effect of two different types of skin flap repair in the treatment of lower limb wounds. Methods Seventy patients with lower limb wounds admitted to the Changzhou Medical District, the 904th Hospital of PLA Joint Logistic Support Force from January 2019 to December 2023 were selected as the study subjects. They were divided into control group and observation group by random number table method, with 35 patients in each group. The control group was repaired with random flap, and the observation group was repaired with medial supramalleolar flap. The excellent and good rate of wound donor site, perioperative index, incidence of adverse reactions and treatment satisfaction were compared between the two groups. Results The excellent and good rate of wound donor site in the observation group was 97.14%, which was higher than 77.14% in the control group (P <0.05). There was no significant difference in perioperative flap area, flap preparation time and operation time between the two groups (P >0.05). The incidence of adverse reactions in the observation group was 5.71%, which was lower than 25.71% in the control group (P <0.05). The treatment satisfaction of the observation group was 100.00%, which was higher than 80.00% of the control group (P <0.05). Conclusion The effect of medial supramalleolar flap repair in patients with lower limb wounds is better than that of random flap repair. The excellent and good rate of wound donor site is higher, which is helpful to promote wound recovery and reduce the incidence of adverse reactions.